Ph.D., Bioinformaitcs

Southern Medical University

ChuangZhou, CN

current - 2019

• Thesis: The development and application of R packages for the analysis and visualization of microbiome downstream data

M.S.,Aquatic Biology

JiMei University

Xiamen, CN

2017 - 2014

• Thesis: The identification and functional classification of circular RNA in the teleost large yellow croaker (Larimichthys crocea)

B.S., Aquaculture

Northwest A&F University

XianYang, CN

2014 - 2010

Senior Bioinformatics Engineer

Xiamen TreatGut Company

XiaMen, CN

2019 - 2017

• Helping build the workflow of microbiome data analysis
• Helping the mining of related microbiome data
• Helping develop the related testing products

Bioinformatics Engineer Intern

Frasergen Genetic Information Company

Wuhan, CN

2016

• Helping the deployment and using with slurm and pbs scheduling systems of the software (PacBio diploid assembler: Falcon, canu, etc) of the TianHe and company’s Supercomputer platform

MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Nature Portfolio. 2022,PREPRINT.

N/A

2022

• S Xu, L Zhan, W Tang, Z Dai, L Zhou, T Feng, M Chen, S Liu, X Fu, T Wu, E Hu, G Yu^*
• Under Review

ggtreeExtra: Compact visualization of richly annotated phylogenetic data

Molecular Biology and Evolution. 2021, 38(9):4039-4042.

N/A

2021

• S Xu, Z Dai, P Guo,X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang^*, X Bo^*, G Yu^*
• Impact Factor = 16.24

Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers

Frontiers in Genetics. 2021, 12:774846.

N/A

• S Xu^#, M Chen^#, T Feng, L Zhan, L Zhou, G Yu^*
• Impact Factor = 4.599

Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis

Aging (Albany NY). 2020, 12(9):8583-8604.

N/A

2020

• J He^#, S Xu^#, B Zhang^#, C Xiao, Z Chen, F Si, J Fu, X Lin, G Zheng^*, G Yu^*, J Chen^*
• Impact Factor = 5.682

Leveraging Fecal Bacterial Survey Data to Predict Colorectal Tumors

Frontiers in Genetics. 2019, 10:447.

N/A

2019

• B Zhang^#,S Xu^#, W Xu^#, Q Chen, Z Chen, C Yan, Y Fan, H Zhang, Q Liu, J Yang, J Yang, C Xiao, H Xu^*, J Ren^*
• Impact Factor = 3.258

Transcriptome-wide identification and functional investigation of circular RNA in the teleost large yellow croaker (Larimichthys crocea)

Marine genomics. 2017, 32:71-78

N/A

2017

• S Xu, S Xiao, C Qiu, Z Wang^*
• Impact Factor = 1.937

ggmsa: a visual exploration tool for multiple sequence alignment and associated data

Briefings in Bioinformatics. 2022.

N/A

2022

• L Zhou^#, T Feng^#, S Xu, F Gao, TT Lam, Q Wang, T Wu, H Huang, L Zhan, L Li, Y Guan, Z Dai^*, G Yu^*
• Impact Factor = 11.622

clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

The Innovation. 2021, 2(3):100141.

N/A

2021

• T Wu^#, E Hu^#, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo^*, G Yu^*

treeio: an R package for phylogenetic tree input and output with richly annotated and associated data

Molecular Biology and Evolution. 2020, 37(2):599-603.

N/A

2020

• LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu^*
• Impact Factor = 16.24

Featured Gut Microbiomes Associated With the Progression of Chronic Hepatitis B Disease

Frontiers in microbiology. 2020, 11:383.

N/A

• Z Chen^#, Y Xie^#, F Zhou, B Zhang, J Wu, L Yang, S Xu, R Stedtfeld, Q Chen, J Liu, X Zhang^*, H Xu^*, J Ren^*
• Impact Factor = 5.64

Preservation of the fecal samples at ambient temperature for microbiota analysis with a cost-effective and reliable stabilizer EffcGut

Science of The Total Environment. 2020, 741:140423.

N/A

• L Yang^#, K Hou^#, B Zhang^#, C Ouyang, A Lin, S Xu, D Ke, L Fang, Q Chen, J Wu, C Yan, Y Lian, T Jiang, J He, H Wang, Y Fu, C Xiao, Z Chen^*
• Impact Factor = 7.963

Genome-wide association study using single marker analysis and Bayesian methods for the gonadosomatic index in the large yellow croaker

Aquaculture. 2018, 486:26-30.

N/A

2018

• Y Gao^#, L Dong^#, S Xu, S Xiao, M Fang, Z Wang^*
• Impact Factor = 3.022

Cloning and expression profiling of gsdf and amh genes in large yellow croaker (Larimichthys crocea)

South China Fisheries Science. 2017, 13(6):1-13.

N/A

2017

• A Lin, Y Xie, S Xu, K Ye, S Gong, Z Wang^*

Identification of a male-specific DNA marker in the large yellow croaker (Larimichthys crocea)

Aquaculture. 2017, 480:116-122.

N/A

• A Lin, S Xiao, S Xu, K Ye, X Lin, S Sun, Z Wang^*
• Impact Factor = 2.71

Rapid construction of genome map for large yellow croaker (Larimichthys crocea) by the whole-genome mapping in BioNano Genomics Irys system

BMC Genomics. 2015, 16(1):1-10

N/A

2015

• S Xiao, J Li, F Ma, L Fang, S Xu, W Chen, Y Wang^*
• Impact Factor = 3.867

国家奖学金

N/A

Southern Medical University,ChuangZhou, CN

2021

Analysis and visualization of microbiome datasets using MicrobiotaProcess

The 10^th BiocAsia2020 Conference, 2020

Virtual Conference

2020